Hi Anselm,
Can you send me the top/crd (1 frame will do) off-list? Thanks.
-Dan
On Tue, Jan 23, 2024 at 5:40 AM Dr. Anselm Horn via AMBER <amber.ambermd.org>
wrote:
> Dear Amber experts,
>
> I set up a solvated protein system using the SIRAH coarse grained force
> field and now try to randomize the ions positions via the randomizeions
> feature in cpptraj.
>
> Unfortunately, my approach, which worked for atomistic topologies, does
> not work here: cpptraj complains about a lacking definition of the
> solvent, although it first seems to recognize it.
> Is there an error in my input file or does randomizeions only work for
> atomistic water models?
>
> The cpptraj input is:
>
> # System definition
> parm r_cg.top [rtop]
> loadcrd r_cg_A.crd [rcrd] parm [rtop]
> # Solvent definition in SIRAH
> solvent :WT4
> crdaction [rcrd] randomizeions :ClW
> go
>
>
>
> The cpptraj output is:
>
> CPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 01/23/24 11:02:32
> | Available memory: 4.489 GB
>
> INPUT: Reading input from 'r_cg_randomizeions.cpptraj'
> [parm r_cg.top [rtop]]
> Reading 'r_cg.top' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> [loadcrd r_cg_A.crd [rcrd] parm [rtop]]
> Reading 'r_cg_A.crd' as Amber Restart
> Loading trajectory 'r_cg_A.crd' as '[rcrd]'
> ----- r_cg_A.crd (1-1, 1) -----
> [solvent :WT4]
> Mask [:WT4] corresponds to 45896 atoms.
> Solvent Mask [:WT4]: 11474 solvent molecules, 45896 solvent atoms
> [crdaction [rcrd] randomizeions :ClW]
> Using set '[rcrd]'
> ----- [rcrd] (1-1, 1) -----
> RANDOMIZEIONS: Swapping postions of ions in mask ':ClW' with solvent.
> No ion can get closer than 3.50 angstroms to another ion.
> RNG: Marsaglia
> Random_Number: seed is <= 0, using wallclock time as seed ( 173917 )
> Error: This command only works if solvent information has been specified.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.1601 seconds.
> Error: Error(s) occurred during execution.
>
>
> Helpful suggestions are appreciated!
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
>
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Received on Tue Jan 23 2024 - 05:30:02 PST
